PDBsum entry: 1cxx

Signaling protein

PDB-id: 1cxx

Contents

Description

Header details

Header records

References

PROCHECK

Protein chain

59 a.a. *

Metal ions

_ZN ×2

* Residue conservation analysis

Tools

Clefts Calculation

PDB id:

1cxx

Name:

Signaling protein

Title:

Mutant r122a of quail cysteine and glycine-rich protein, nmr, minimized structure

Structure:

Cysteine and glycine-rich protein crp2. Chain: a. Fragment: carboxyl-terminal lim-domain. Engineered: yes. Mutation: yes

Source:

Coturnix japonica. Japanese quail. Organism_taxid: 93934. Cell: fibroblast. Expressed in: escherichia coli. Expression_system_taxid: 562.

UniProt:

Q05158 (CSRP2_COTJA)

Seq:

194 a.a.

Struc:

59 a.a.*

Key:	PfamA domain
Secondary structure	CATH domain

* PDB and UniProt seqs differ at 1 residue position (black cross)

Resolution:

not givenÅ

NMR structure:

1 models

Authors:

K.Kloiber,R.Weiskirchen,B.Kraeutler,K.Bister,R.Konrat

Key ref:

K.Kloiber et al. (1999). Mutational analysis and NMR spectroscopy of quail cysteine and glycine-rich protein CRP2 reveal an intrinsic segmental flexibility of LIM domains.. J Mol Biol, 292, 893-908. [PubMed id: 10525413] [DOI: 10.1006/jmbi.1999.3118]

Date:

31-Aug-99

Release date:

08-Sep-99

Related entries:

1qli
related wild-type peptide: carboxylterminal lim domain of
qcrp2

Quick_links

Procheck

Clefts

Surface

Key reference

DOI no: 10.1006/jmbi.1999.3118

J Mol Biol 292:893-908 (1999)

PubMed id: 10525413

Mutational analysis and NMR spectroscopy of quail cysteine and glycine-rich protein CRP2 reveal an intrinsic segmental flexibility of LIM domains.

K.Kloiber, R.Weiskirchen, B.Kräutler, K.Bister, R.Konrat.

ABSTRACT

The LIM domain is a conserved cysteine and histidine-containing structural module of two tandemly arranged zinc fingers. It has been identified in single or multiple copies in a variety of regulatory proteins, either in combination with defined functional domains, like homeodomains, or alone, like in the CRP family of LIM proteins. Structural studies of CRP proteins have allowed a detailed evaluation of interactions in LIM-domains at the molecular level. The packing interactions in the hydrophobic core have been identified as a significant contribution to the LIM domain fold, whereas hydrogen bonding within each single zinc binding site stabilizes zinc finger geometry in a so-called "outer" or "indirect" coordination sphere. Here we report the solution structure of a point-mutant of the carboxyl-terminal LIM domain of quail cysteine and glycine-rich protein CRP2, CRP2(LIM2)R122A, and discuss the structural consequences of the disruption of the hydrogen bond formed between the guanidinium side-chain of Arg122 and the zinc-coordinating cysteine thiolate group in the CCHC rubredoxin-knuckle. The structural analysis revealed that the three-dimensional structure of the CCHC zinc binding site in CRP2(LIM2)R122A is adapted as a consequence of the modified hydrogen bonding pattern. Additionally, as a result of the conformational rearrangement of the zinc binding site, the packing interactions in the hydrophobic core region are altered, leading to a change in the relative orientation of the two zinc fingers with a concomitant change in the solvent accessibilities of hydrophobic residues located at the interface of the two modules. The backbone dynamics of residues located in the folded part of CRP2(LIM2)R122A have been characterized by proton-detected(15)N NMR spectroscopy. Analysis of the R2/R1ratios revealed a rotational correlation time of approximately 6.2 ns and tumbling with an axially symmetric diffusion tensor (D parallel/D perpendicular=1.43). The relaxation data were also analyzed using a reduced spectral density mapping approach. As in wild-type CRP2(LIM2), significant mobility on a picosecond/nanosecond time-scale was detected, and conformational exchange on a microsecond time-scale was identified for residues located in loop regions between secondary structure elements. In summary, the relative orientation of the two zinc binding sites and the accessibility of hydrophobic residues is not only determined by hydrophobic interactions, but can also be modified by the formation and/or breakage of hydrogen bonds. This may be important for the molecular interactions of an adaptor-type LIM domain protein in macromolecular complexes, particularly for the modulation of protein-protein interactions.

Selected figure(s)

Figure 4.
Figure 4. Solution structure of CRP2(LIM2)R122A. Ribbon diagram (left) of a selected representative structure from the calculated set for CRP2(LIM2)R122A (residues 118 to 174). Separate matches for each of the two zinc binding sites encompassing residues 120 to 145 (middle) or residues 146 to 173 (right), respectively, indicate residual mobility between the two zinc finger subdomains. The diagrams were produced using the program MOLMOL [Koradi et al 1996].

Figure 9.
Figure 9. Schematic representation showing the change in the relative orientation of the two CCHC and CCCC zinc-binding sites in CRP2(LIM2)R122A introduced by the point mutation at residue position 122. (a) Ribbon drawing showing the superposition of a representative structure taken from the ensemble of 11 energy-minimized NMR structures of CRP2(LIM2)R122A (yellow) and the wild-type CRP2(LIM2) structure with the lowest residual restraint violations [Konrat et al 1997] (blue). Backbone atoms of the N-terminal CCHC zinc finger encompassing residues Cys120-Cys144 were matched. (b) Orthogonal view displaying only the C-terminal CCCC zinc binding site of mutant CRP2(LIM2)R122A (yellow) and wild-type protein (blue). The pictures were produced with the program MOLMOL [Koradi et al 1996].

The above figures are reprinted by permission from Elsevier: J Mol Biol (1999, 292, 893-908) copyright 1999.

Figures were selected by an automated process.